Educational · Protein-Ligand Masterclass

Learn molecular dynamics simulation the way it's actually used in research.

A hands-on workshop in MD simulation and protein-ligand docking, taught by someone who runs these pipelines for a living — not a lecture series, a working session where you build the skill.

Watch the 2-minute overview
Who this is for

Built for people who need to run MD, not just read about it.

This is a fit if

  • You're a graduate student, postdoc, or researcher who needs simulation results for a paper or thesis and doesn't yet have the workflow.
  • You're new to molecular dynamics and want a guided, structured path instead of piecing it together from scattered tutorials.
  • You're on an industry team evaluating whether MD and AI-augmented modeling belong in your pipeline.
  • You learn best by running the simulation yourself, with support when you get stuck.

Probably not a fit if

  • You're looking for someone to run the simulation for you — that's the Research Simulation Package, not this workshop.
  • You want a passive video course with no independent project or feedback.
  • You're already deep into production MD pipelines and need custom implementation, not training.
What you'll learn

From first principles to your own independent project.

The workshop moves in order — each session builds on the last, ending with a project you scope and run yourself.

01

Foundations of molecular dynamics

What MD simulation actually shows you that a static structure can't, and the core concepts you need before touching a tool: force fields, energy minimization, equilibration.

02

Protein-ligand docking

Setting up and running docking, interpreting binding poses, and knowing when a result is trustworthy versus an artifact.

03

AI-augmented modeling tools

Where modern ML tools speed up the workflow, and where they still need a human checking the physics.

04

Independent project

You apply everything to your own molecule or a guided case study, with support available as you work through it — this is where the training actually sticks.

What past participants say

Trusted by researchers stepping into MD for the first time.

"The lectures of Omar were profound yet simple to digest. In summary, he effectively taught a comprehensive content that often overwhelms learners, providing a clear path to navigate without getting lost and diverted. As a starter in MD, I highly recommend Omar."

Aaron Hernandez-Cid, PhD, Analytical Biochemist

"I recently was mentored by Omar during his molecular dynamics workshop. As a novice to the subject I was guided through the process step by step. The independent project section of the course is especially useful, allowing you to apply what you have learnt with extra support available if needed."

Morgan Grainger, Postgraduate Researcher, University of Northampton
Pricing

Two seats, one workshop.

Same curriculum either way — pricing reflects who's sending you.

Academia
$799
  • Full Protein-Ligand Masterclass curriculum
  • Independent project with feedback
  • For students, postdocs & academic researchers
Reserve your seat →
Not sure this is the right fit yet?

Book a free exploratory call and we'll figure out whether this workshop, the Research Simulation Package, or something else is the right starting point.

Book a call →